GOG already offers this exact functionality, two different ways:
1. Add a fourth SKU. There are no files associated with this new SKU, but if you own it, you can download the files associated with the first three SKUs.
2. When you pay for the products, if all three SKUs are in your shopping cart[1], you get a 25% discount. Otherwise you pay full price.
If I'm reading you right, you're saying that if you bought bundle #2, then refunding the $10 item should obviously get you $7.50 -- because that's what you paid for it when you bought it -- but there's just no way of determining how to refund the same $10 item from bundle #1, even though bundle #1 and bundle #2 do not differ in any way at all.
(In fact, GOG bundles usually price the last item negatively -- it is cheaper to buy the whole bundle than it would be to buy all-but-one of the bundled items. These are still all formally individual purchases covered by the return policy, and I feel pretty confident they're not going to refund you a negative amount if you return an item you bought in one of these individual-purchases-with-discount bundles.)
[1] Technical note that doesn't affect the discussion: if you already own an item, it counts as being in your shopping cart for purposes of bundle discounts.